Variant report

Variant	rs1319633
Chromosome Location	chr12:60750047-60750048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1021887	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784046	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877403	0.81[CHD][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs10877412	0.83[EUR][1000 genomes]
rs10877413	0.85[EUR][1000 genomes]
rs10877414	0.86[EUR][1000 genomes]
rs10877422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877425	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11173389	0.83[EUR][1000 genomes]
rs11173391	0.85[EUR][1000 genomes]
rs11173392	0.85[EUR][1000 genomes]
rs11173393	0.85[EUR][1000 genomes]
rs11173395	0.86[EUR][1000 genomes]
rs11173397	0.86[EUR][1000 genomes]
rs11173398	0.86[EUR][1000 genomes]
rs11173405	0.85[EUR][1000 genomes]
rs11173407	0.83[EUR][1000 genomes]
rs11173414	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173416	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11173418	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173437	0.88[EUR][1000 genomes]
rs11173438	0.88[EUR][1000 genomes]
rs11173439	0.88[EUR][1000 genomes]
rs1119988	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11536139	0.83[EUR][1000 genomes]
rs11561446	0.85[EUR][1000 genomes]
rs11561447	0.85[EUR][1000 genomes]
rs11836206	0.85[EUR][1000 genomes]
rs12228227	0.91[EUR][1000 genomes]
rs12228889	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12230599	0.81[EUR][1000 genomes]
rs12231371	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12580142	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12580151	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1394328	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1394330	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1504459	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504460	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1504462	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504463	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504464	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532810	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1532811	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1566847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1580916	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1604865	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1604866	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1604867	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1604868	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1604869	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17606011	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17606158	0.88[EUR][1000 genomes]
rs17606266	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17606387	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17606458	0.91[EUR][1000 genomes]
rs17669416	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1827638	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1857730	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1875860	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1995515	0.84[EUR][1000 genomes]
rs2102257	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2102258	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs2202365	0.83[EUR][1000 genomes]
rs2221407	0.86[EUR][1000 genomes]
rs2262939	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2363587	0.89[EUR][1000 genomes]
rs2363600	0.85[EUR][1000 genomes]
rs2455998	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2655842	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2655843	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2655846	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2655848	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2655856	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2655871	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2655886	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2655893	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2655899	0.80[ASN][1000 genomes]
rs2731465	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2731487	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2731488	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2731491	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731492	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920119	0.85[EUR][1000 genomes]
rs4353306	0.86[EUR][1000 genomes]
rs4583008	0.89[EUR][1000 genomes]
rs4616072	0.86[EUR][1000 genomes]
rs4638340	0.83[EUR][1000 genomes]
rs4758863	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55810124	0.89[EUR][1000 genomes]
rs56088032	0.87[EUR][1000 genomes]
rs56173629	0.86[EUR][1000 genomes]
rs56240683	0.85[EUR][1000 genomes]
rs60691341	0.86[EUR][1000 genomes]
rs60798845	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61923155	0.84[EUR][1000 genomes]
rs6581310	0.84[EUR][1000 genomes]
rs6581318	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136994	0.84[EUR][1000 genomes]
rs7295183	0.84[EUR][1000 genomes]
rs7306226	0.85[EUR][1000 genomes]
rs7307028	0.90[EUR][1000 genomes]
rs7952971	0.86[EUR][1000 genomes]
rs7953857	0.84[EUR][1000 genomes]
rs7957295	0.82[EUR][1000 genomes]
rs7960292	0.85[EUR][1000 genomes]
rs7960303	0.85[EUR][1000 genomes]
rs7960487	0.85[EUR][1000 genomes]
rs7961791	0.89[EUR][1000 genomes]
rs7961816	0.84[EUR][1000 genomes]
rs7963214	0.80[ASN][1000 genomes]
rs7971143	0.80[ASN][1000 genomes]
rs7971161	0.89[EUR][1000 genomes]
rs7972668	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7973156	0.84[EUR][1000 genomes]
rs7975549	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs924836	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899137	chr12:60568891-60797083	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1054287	chr12:60601870-60861866	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv832431	chr12:60626292-60809233	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1047466	chr12:60702221-61521156	Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv983465	chr12:60721408-60752940	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2762983	chr12:60735475-60767081	Enhancers Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1319633	RDH5	cis	parietal	SCAN
rs1319633	CNPY2	cis	parietal	SCAN
rs1319633	OBFC2B	cis	parietal	SCAN

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60750000-60750400	Enhancers	Fetal Intestine Large	intestine

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